X-ray crystallographic study of several 2′-deoxy-β-d-ribonucleosides with 1-deazapurine-derived aglycones

The 2′-deoxy-β-d-ribonucleosides of 1,3-deazapurine (benzimidazole (1)), 1-deazapurine (both 1H-imidazo[4,5-b]pyridine (2) and 3H-imidazo[4,5-b]pyridine (3)), and 6-benzoylamino-1-deazapurine (7-benzoylamino-3H-imidazo[4,5-b]pyridine (4)) have been prepared and structurally characterized by X-ray crystallography. Especially compounds 1–3 can serve as artificial nucleosides that may substitute 2′-deoxy adenosine because they lack the exocyclic amino group and one or two of the endocyclic nitrogen atoms and hence have a much smaller potential to engage in hydrogen bonds. In the latter respect, they are candidates for nucleosides in metal-ion mediated base pairs. The unit cell of compound 3 contains two crystallographically independent molecules. Compound 4 was crystallized from methanol and water, respectively, giving rise to two different solvates. Despite the closely related aglycones, the sugar conformations in 1–4 are found to be highly variable (1: 2T1; 2: 3T2; 3: 3E and E4; 4: 2E and 2T3). The structures reported here confirm that there is no simple correlation between the sugar conformation and the character of the nucleoside, and they will hopefully contribute to a better understanding of the complex interplay of different effects that are in control of the conformational equilibrium

Solution structure of a DNA double helix with consecutive metal-mediated base pairs

Metal-mediated base pairs represent a powerful tool for the site-specific functionlization of nucleic acids with metal ions. The development of applications of the metal-modified nucleic acids will depend on the availability of structural information on these double helices. We present here the NMR solution structure of a self-complementary DNA oligonucleotide with three consecutive imidazole nucleotides in its centre. In the absence of transition-metal ions, a hairpin structure is adopted with the artifical nucleotides forming the loop. In the presence of Ag(I) ions, a duplex comprising three imidazole-Ag+-imidazole base pairs is formed. Direct proof for the formation of metal-mediated base pairs was obtained from (1)J(N-15,Ag-107/109) couplings upon incorporation of N-15-labelled imidazole. The duplex adopts a B-type conformation with only minor deviations in the region of the artifical bases. This work represents the first structural characterization of a metal-modified nucleic acid with a continuous stretch of metal-mediated base pairs